There is a quite interesting way to execute script minimized by making him restart itself minimised. Here is the code to put in the beginning of your script:

if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
... script logic here ...
exit

How it works

When the script is being executed IS_MINIMIZED is not defined (if not DEFINED IS_MINIMIZED) so:

1. IS_MINIMIZED is set to 1: set IS_MINIMIZED=1.

2. Script starts a copy of itself using start command && start "" /min "%~dpnx0" %* where:

   1. "" - empty title for the window.
   2. /min - switch to run minimized.
   3. "%~dpnx0" - full path to your script.
   4. %* - passing through all your script's parameters.

3. Then initial script finishes its work: && exit.

For the started copy of the script variable IS_MINIMISED is set by the original script so it just skips the execution of the first line and goes directly to the script logic.

Remarks

• You have to reserve some variable name to use it as a flag.
• The script should be ended with exit, otherwise the cmd window wouldn't be closed after the script execution.

• If your script doesn't accept arguments you could use argument as a flag instead of variable:

  if "%1" == "" start "" /min "%~dpnx0" MY_FLAG && exit